CyTOF immune profiling of chikungunya virus infection - clustered data

The goal of this study was to comprehensively analyze the peripheral immune response to acute chikungunya virus infection. Blood samples were collected as part of a hospital-based study of dengue and chikungunya in the Nicaraguan National Pediatric Reference Hospital in Managua, Nicaragua. The study includes samples collected from a total of 42 pediatric cases with detectable CHIKV viremia presenting to the hospital between November 2014 and October 2015 were included. Paired PBMC samples were collected at acute (1-2 d post symptom onset) and convalescent (15-17 d post symptom onset) infection timepoints for a total of 84 samples. The samples were analyzed by mass cytometry to broadly characterize the immune profile at each timepoint. Conclusion: We find several associations between immune cell subsets that change in frequency and phenotype between the acute and convalescent phases of infection, most notably monocytes Notes: This experiment is a duplication of FR-FCM-ZYTZ, however the FCS files have been clustered and annotated using the FlowSOM package implemented through the Astrolabe Cytometry Platform (Astrolabe Diagnostics, Inc.). Single cell clustering annotations at two resolutions (assignment and profiling) are embedded as channels in the FCS files. The attached "assignment" and "profiling" csvs are keys that map the numbered clusters to their corresponding annotations. Paired acute and convalescent samples were barcoded using CD45 antibodies conjugated to distinct isotopes and pooled prior to staining to minimize technical variability during staining and data acquisition